The awk below runs and produces the following output on the file2 . This is just an example of the format as the file is ~14MB. file1.txt is attached. I am trying to count the ids that match between the two files and out the ids that are missing. Thank you :).
file2
970 NM_213590 chr13 + 50571142 50592603 50586076 50587300 2 50571142,50586070, 50571899,50592603, 0 TRIM13 cmpl cmpl -1,0,
2166 NM_001017364 chr1 + 207262583 207273337 207262876 207273274 6 207262583,207263655,207264988,207269866,207271494,207273133, 207262934,207263826,207265165,207269960,207271609,207273337, 0 C4BPB cmpl cmpl 0,1,1,1,2,0,
1044 NM_152866 chr11 + 60223281 60238225 60229847 60235941 8 60223281,60228544,60229657,60230474,60231760,60233393,60234431,60235722, 60223418,60228633,60230006,60230594,60231817,60233630,60234533,60238225, 0 MS4A1 cmpl cmpl -1,-1,0,0,0,0,0,0,
1274 NM_020466 chr6 - 90341942 90348474 90346991 90348435 3 90341942,90347460,90348390, 90347072,90347601,90348474, 0 LYRM2 cmpl cmpl 0,0,0,
162 NM_014912 chr10 - 93808396 94050875 93811968 94000107 10 93808396,93841076,93851586,93870832,93902785,93904701,93940719,93952233,93999102,94050682, 93812196,93841258,93851701,93870951,93902875,93904842,93940776,93952393,94000118,94050875, 0 CPEB3 cmpl cmpl 0,1,0,1,1,1,1,0,0,-1,
1241 NM_015613 chr10 - 85991275 86001217 85991682 86001195 4 85991275,85993828,85996975,86001073, 85992659,85994134,85997442,86001217, 0 LRIT1 cmpl cmpl 1,1,2,0,
1962 NM_206880 chr5 + 180581942 180582890 180581942 180582890 1 180581942, 180582890, 0 OR2V2 cmpl cmpl 0,
205 NM_020464 chr6 - 138743180 138893668 138745217 138893048 7 138743180,138750847,138751529,138768137,138794442,138817355,138892846, 138745953,138750980,138754817,138768330,138794570,138817508,138893668, 0 NHSL1 cmpl cmpl 2,1,1,0,1,1,0,
116 NM_001193342 chr20 - 45186461 45280100 45188660 45242181 13 45186461,45192052,45194867,45204211,45212210,45216697,45217798,45221042,45224795,45228609,45239084,45242098,45279949, 45188837,45192190,45195029,45204324,45212308,45216802,45217894,45221168,45224981,45228676,45239248,45242191,45280100, 0 SLC13A3 cmpl cmpl 0,0,0,1,2,2,2,2,2,1,2,0,-1,
1038 NM_152716 chr11 - 59404191 59436511 59405862 59436368 19 59404191,59406520,59406764,59410352,59415226,59416934,59418226,59419016,59419936,59420310,59421455,59422995,59423428,59423971,59425002,59426338,59426724,59434325,59436353, 59405884,59406670,59406856,59410508,59415386,59417083,59418286,59419114,59420060,59420491,59421545,59423213,59423518,59424073,59425197,59426419,59426942,59434437,59436511, 0 PATL1 cmpl cmpl 2,2,0,0,2,0,0,1,0,2,2,0,0,0,0,0,1,0,0,
2041 NM_198184 chr3 + 190930321 190967910 190930321 190967910 3 190930321,190936535,190967825, 190930423,190936750,190967910, 0 OSTN cmpl cmpl 0,0,2,
1022 NM_198183 chr11 - 57319127 57335803 57319830 57322021 4 57319127,57321909,57327809,57335321, 57319982,57322096,57327905,57335803, 0 UBE2L6 cmpl cmpl 1,0,-1,-1,
735 NR_037612 chr22 + 19705991 19712297 19712297 19712297 12 19705991,19707124,19707328,19707637,19707842,19708071,19708290,19709162,19709344,19709759,19709950,19711376, 19706094,19707221,19707415,19707761,19707977,19708189,19708392,19709259,19709480,19709862,19711102,19712297, 0 SEPT5-GP1BB unk unk -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
735 NR_037611 chr22 + 19704742 19712297 19712297 19712297 12 19704742,19707124,19707328,19707637,19707842,19708071,19708290,19709162,19709344,19709759,19709950,19711376, 19706341,19707221,19707415,19707761,19707977,19708189,19708392,19709259,19709480,19709862,19711102,19712297, 0 SEPT5-GP1BB unk unk -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
awk
awk 'NR==FNR{a[$1];next}
$13 in a{c++; delete a[$13]}
END{if(c) print c " ids found";
for(k in a) print k " missing"}' file1.txt file2 > output
output
4602 ids found
POMK-SGK196 missing
ACKR1 missing
POMGNT2-GTDC2 missing
However when I do wc -l file1 there are 4609 lines. Is there a better way to find what count is common and output the missing. Thank you :).